R Observatory: Metrics for dynwrap version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dynwrap

1.3.0Package record

Representing and Inferring Single-Cell Trajectories

0packages dependsuggested by 1

9.2Kdownloads / year

81.0%test coverage

13/13flavors OK

Overview

About

Maintained by Robrecht CannoodtCRAN page ↗GitHub ↗Issues ↗

Provides functionality to infer trajectories from single-cell data, represent them into a common format, and adapt them. Other biological information can also be added, such as cellular grouping, RNA velocity and annotation. Saelens et al. (2019) doi:10.1038/s41587-019-0071-9.

Changes in 1.3.0

MODERNISATION: Replace %>% pipes with native |> pipe throughout.
MODERNISATION: Remove magrittr dependency; replace set_rownames()/set_colnames() with base R assignments.
MODERNISATION: Replace deprecated dplyr::do() with reframe().
MODERNISATION: Replace deprecated mutate_at() with mutate(across()).
FIX: Add missing "id" to globalVariables() to silence R CMD check NOTE about no visible binding for global variable id.
FIX: Replace relative cross-vignette URLs (../create_ti_method_xxx) with proper file-relative links to silence R CMD check NOTE.
MINOR CHANGE: Update GitHub Actions workflows to use actions/checkout@v6 and actions/upload-artifact@v7.
MINOR CHANGE: Add pkgdown.yaml GitHub Actions workflow for website deployment.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("dynwrap", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("dynverse/dynwrap")

Development version from dynverse/dynwrap. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-dynwrap

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-dynwrap

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-dynwrap

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK9 OK2026-04-02

Show 1 earlier changeHide 1 earlier change

NOTE5 OK, 9 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.0

READMEYes · 279 wordsVignettesYes · 4 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 1.3.0Citation fileYes · cites a publication

Help pages: 68 (3 internal)includes a package overview page
Examples that run: 98%47 run in a plain check (1 of them under a condition) · 1 hold no code
Exported functions with examples: 76%
Documented parameters: 98%
Return-value docs: 78%
Help pages citing references: 0%

Vignettes (4)

Creating a TI method: Container HTML
Creating a TI method: R HTML
Creating a TI method: Script HTML
Creating a TI method: Wrapping trajectories HTML

How these are measured

Downloads

9.2K

CRAN downloads in the past year

Rank #4,569 · ~25/day · ~767/mo

Releases R versions

Daily download trend is not available in this view yet.

59630 days

1.8K90 days

9.2K1 year

Compare downloads with other packages →

Also on388 r2u5 autocran51 c2d4u

How downloads are counted

Repository

dynverse/dynwrap ↗Organization: dynverse

20Stars

5Forks

17Open issues

0Open PRs

3Releases

1,656Commits

5Commit identities

trajectory-inference

1,656 commits · Last activity 2026-03-31 · +5.3% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 97%
Median days to close, 50 most recently updated closed issues: 9
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-25 · 172026-09-22 · 20

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/dynverse/dynwrap on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2019-03-04

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 3 practices

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing dynwrap adds 49 packages (30 with compiled code, 32 MB of source tarballs). Heaviest: stringi 11 MB, igraph 4.8 MB, Rcpp 1.8 MB.

Depends (1)

R >= 4.1.0

Imports (18)

assertthat babelwhale crayon dplyr dynutils dynparam igraph glueMatrixmethodspurrr processx readr stringr reshape2 tibble tidyr yaml

LinkingTo (0)

none

Suggests (8)

covr dyndimred hdf5r knitr pkgload ranger rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

dyngen

How these are counted

Code & Tests

Datasets

People & History

People (2)

Robrecht Cannoodt

Author, Maintainer since 1.1.4 (2019)

Wouter Saelens

Author

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-04-01
1.3.0Latest
record
2026-03-31 · current release · diff ↗
archivedRemoved from CRAN
2026-03-25
issues were not corrected despite reminders
1.2.5
record
2025-11-26 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2023-07-19
1.2.4
record
2023-07-19 · diff ↗
archivedRemoved from CRAN
2023-07-09
requires archived package 'babelwhale'
R
R 4.3.0 released · 2023-04-21
1.2.3
record
2023-03-01 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.2.2
record
2021-03-23 · diff ↗ ·
added 2 exports
add_feature_importance, is_wrapper_with_feature_importance
1.2.1
record
2020-05-14 · diff ↗

Show 6 earlier eventsHide 6 earlier events

R
R 4.0.0 released · 2020-04-24
unarchivedReturned to CRAN
2020-03-09
1.2.0
record
2020-03-09 · diff ↗ ·
removed 1 export
orient_topology_to_velocity

added 2 exports
add_regulatory_network, remove_root
archivedRemoved from CRAN
2020-03-05
check problems were not corrected despite reminder Does not use 'Suggests: dyndimred' conditionally
1.1.4
record
2019-10-11
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-10-11
Total releases: 8 / 7 yrs
License: MIT + file LICENSE OSI · relicensed from GPL-3 in 1.2.0
Minimum R: ≥ 4.1.0
Bundled data: 62 KB / 9 files
Download size: 1.9 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("dynwrap")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1038/s41587-019-0071-9.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for dynwrap version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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